Difference between revisions of "Ss"

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(New page: A command to list a summary of the secondary structure for a selection. Use like "ss my_protein" where "my_protein" is the name of the chain or structure in view. <source lang="python"> def ss(selectio...)
 
m (changed a loop variable to avoid name clashes.)
Line 19: Line 19:
 
     sses = [SSE(num, currentType)]
 
     sses = [SSE(num, currentType)]
 
     currentSSE = sses[0]
 
     currentSSE = sses[0]
     for resi, ss in stored.pairs:
+
     for resi, ssType in stored.pairs:
         if ss == currentType:
+
         if ssType == currentType:
 
             currentSSE.end = resi
 
             currentSSE.end = resi
 
         else:
 
         else:
             sses.append(SSE(resi, ss))
+
             sses.append(SSE(resi, ssType))
 
             currentSSE = sses[-1]
 
             currentSSE = sses[-1]
             currentType = ss
+
             currentType = ssType
  
 
     for sse in sses:
 
     for sse in sses:

Revision as of 12:56, 9 October 2007

A command to list a summary of the secondary structure for a selection. Use like "ss my_protein" where "my_protein" is the name of the chain or structure in view.

def ss(selection):

    class SSE(object):

        def __init__(self, start, typ):
            self.start, self.typ = start, typ
            self.end = -1

        def __repr__(self):
            return "%s-%s %s" % (self.start, self.end, self.typ)

    stored.pairs = []
    cmd.iterate(selection, "stored.pairs.append((resi, ss))")
    num, currentType = stored.pairs[0]

    sses = [SSE(num, currentType)]
    currentSSE = sses[0]
    for resi, ssType in stored.pairs:
        if ssType == currentType:
            currentSSE.end = resi
        else:
            sses.append(SSE(resi, ssType))
            currentSSE = sses[-1]
            currentType = ssType

    for sse in sses:
        print sse

cmd.extend("ss", ss)